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Searched refs:atomIds (Results 1 – 25 of 44) sorted by relevance

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/dports/textproc/fox-xml/fox-4.1.2-91-g9c6716e/wcml/
H A Dm_wcml_molecule.F90366 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i)))
409 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i)))
454 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i)))
500 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i)))
543 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i)))
586 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i)))
631 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i)))
677 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i)))
1083 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i)))
1126 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i)))
[all …]
H A Dm_wcml_molecule.m437 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i)))
49 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i)))
62 character(len=*), intent(in), optional :: atomIds(:)
81 if (present(atomIds)) then
125 if (present(atomIds)) then
151 character(len=*), intent(in), optional :: atomIds(:)
170 if (present(atomIds)) then
216 if (present(atomIds)) then
237 character(len=*), intent(in), optional :: atomIds(:)
288 character(len=*), intent(in), optional :: atomIds(:)
[all …]
/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/
H A DAllChem.py111 def GetConformerRMS(mol, confId1, confId2, atomIds=None, prealigned=False): argument
131 if atomIds:
132 AlignMolConformers(mol, confIds=[confId1, confId2], atomIds=atomIds)
147 def GetConformerRMSMatrix(mol, atomIds=None, prealigned=False): argument
179 if atomIds:
180 AlignMolConformers(mol, atomIds=atomIds, RMSlist=rmsvals)
186 GetConformerRMS(mol, confIds[0], confIds[i], atomIds=atomIds, prealigned=prealigned))
192 cmat.append(GetConformerRMS(mol, confIds[i], confIds[j], atomIds=atomIds, prealigned=True))
/dports/science/rdkit/rdkit-Release_2021_03_5/Contrib/IFG/
H A DREADME18 # return the list of IFG (atomIds, atoms & type) for a molecule object:
24 [IFG(atomIds=(2,), atoms='n', type='cnc'),
25 IFG(atomIds=(4, 5, 6, 7), atoms='NS(=O)=O', type='cNS(c)(=O)=O'),
26 IFG(atomIds=(12,), atoms='N', type='cN'),
27 IFG(atomIds=(15,), atoms='n', type='cnc')]
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolAlign/
H A DAlignMolecules.cpp191 const std::vector<unsigned int> *atomIds = nullptr) { in _fillAtomPositions() argument
194 if (atomIds == nullptr) { in _fillAtomPositions()
201 pts.reserve(atomIds->size()); in _fillAtomPositions()
203 for (cai = atomIds->begin(); cai != atomIds->end(); cai++) { in _fillAtomPositions()
209 void alignMolConformers(ROMol &mol, const std::vector<unsigned int> *atomIds, in alignMolConformers() argument
224 _fillAtomPositions(refPoints, refCnf, atomIds); in alignMolConformers()
239 _fillAtomPositions(prbPoints, *(*cnfi), atomIds); in alignMolConformers()
257 _fillAtomPositions(prbPoints, conf, atomIds); in alignMolConformers()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Descriptors/
H A DUSRDescriptor.cpp162 std::vector<std::vector<unsigned int>> &atomIds) { in getAtomIdsForFeatures() argument
164 PRECONDITION(atomIds.size() == numFeatures, in getAtomIdsForFeatures()
178 atomIds[i].push_back(mi.second); in getAtomIdsForFeatures()
215 std::vector<std::vector<unsigned int>> &atomIds, int confId) { in USRCAT() argument
227 unsigned int numClasses = atomIds.size(); in USRCAT()
230 atomIds.resize(numClasses); in USRCAT()
231 getAtomIdsForFeatures(mol, atomIds); in USRCAT()
252 for (const auto &atomsInClass : atomIds) { in USRCAT()
/dports/math/vtk9/VTK-9.1.0/Domains/Chemistry/
H A DvtkMoleculeMapper.cxx244 vtkSelection* selection, vtkIdTypeArray* atomIds, vtkIdTypeArray* bondIds) in GetSelectedAtomsAndBonds() argument
247 if (selection == nullptr || (atomIds == nullptr && bondIds == nullptr)) in GetSelectedAtomsAndBonds()
253 if (atomIds != nullptr) in GetSelectedAtomsAndBonds()
255 atomIds->Reset(); in GetSelectedAtomsAndBonds()
285 if (atomIds != nullptr && curId < numAtoms) // atoms in GetSelectedAtomsAndBonds()
287 atomIds->InsertNextValue(curId); in GetSelectedAtomsAndBonds()
642 vtkIdType atomIds[2]; in UpdateBondGlyphPolyData() local
657 atomIds[0] = bond.GetBeginAtomId(); in UpdateBondGlyphPolyData()
658 atomIds[1] = bond.GetEndAtomId(); in UpdateBondGlyphPolyData()
761 cylColors->InsertNextTuple(atomIds[0], atomColorArray); in UpdateBondGlyphPolyData()
[all …]
H A DvtkMoleculeMapper.h263 vtkSelection* selection, vtkIdTypeArray* atomIds, vtkIdTypeArray* bondIds);
264 virtual void GetSelectedAtoms(vtkSelection* selection, vtkIdTypeArray* atomIds) in GetSelectedAtoms() argument
266 this->GetSelectedAtomsAndBonds(selection, atomIds, nullptr); in GetSelectedAtoms()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/MinimalLib/
H A Djswrapper.cpp25 std::vector<int> &atomIds,
58 std::vector<int> atomIds; in draw_to_canvas_with_highlights() local
69 atomIds, bondIds); in draw_to_canvas_with_highlights()
80 MolDraw2DUtils::prepareAndDrawMolecule(*d2d, *self.d_mol, legend, &atomIds, in draw_to_canvas_with_highlights()
H A Dminilib.cpp45 std::string &legend, std::vector<int> &atomIds, in process_details() argument
57 atomIds.push_back(molval.GetInt()); in process_details()
148 std::vector<int> atomIds; in svg_() local
154 atomIds, bondIds); in svg_()
166 MolDraw2DUtils::prepareAndDrawMolecule(drawer, m, legend, &atomIds, &bondIds); in svg_()
/dports/math/vtk6/VTK-6.2.0/Domains/Chemistry/
H A DvtkMoleculeMapper.h193 vtkIdTypeArray *atomIds,
196 vtkIdTypeArray *atomIds) in GetSelectedAtoms() argument
198 this->GetSelectedAtomsAndBonds(selection, atomIds, NULL); in GetSelectedAtoms()
H A DvtkMoleculeMapper.cxx226 vtkIdTypeArray *atomIds, in GetSelectedAtomsAndBonds() argument
230 if (selection == NULL || (atomIds == NULL && bondIds == NULL) ) in GetSelectedAtomsAndBonds()
236 if (atomIds != NULL) in GetSelectedAtomsAndBonds()
238 atomIds->Reset(); in GetSelectedAtomsAndBonds()
269 if (atomIds != NULL && curId < numAtoms) // atoms in GetSelectedAtomsAndBonds()
271 atomIds->InsertNextValue(curId); in GetSelectedAtomsAndBonds()
/dports/math/vtk8/VTK-8.2.0/Domains/Chemistry/
H A DvtkMoleculeMapper.h256 vtkIdTypeArray *atomIds,
259 vtkIdTypeArray *atomIds) in GetSelectedAtoms() argument
261 this->GetSelectedAtomsAndBonds(selection, atomIds, nullptr); in GetSelectedAtoms()
H A DvtkMoleculeMapper.cxx245 vtkIdTypeArray *atomIds, in GetSelectedAtomsAndBonds() argument
249 if (selection == nullptr || (atomIds == nullptr && bondIds == nullptr) ) in GetSelectedAtomsAndBonds()
255 if (atomIds != nullptr) in GetSelectedAtomsAndBonds()
257 atomIds->Reset(); in GetSelectedAtomsAndBonds()
288 if (atomIds != nullptr && curId < numAtoms) // atoms in GetSelectedAtomsAndBonds()
290 atomIds->InsertNextValue(curId); in GetSelectedAtomsAndBonds()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Wrap/
H A DStereoGroup.cpp31 python::object atomIds) { in createStereoGroup() argument
33 python::stl_input_iterator<unsigned int> beg(atomIds), end; in createStereoGroup()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Subgraphs/
H A DSubgraphUtils.cpp112 PATH_TYPE bondListFromAtomList(const ROMol &mol, const PATH_TYPE &atomIds) { in bondListFromAtomList() argument
114 unsigned int natms = atomIds.size(); in bondListFromAtomList()
120 const Bond *bnd = mol.getBondBetweenAtoms(atomIds[i], atomIds[j]); in bondListFromAtomList()
/dports/math/vtk9/VTK-9.1.0/Rendering/RayTracing/
H A DvtkOSPRayMoleculeMapperNode.cxx220 vtkIdType atomIds[2]; in Render() local
239 atomIds[0] = bond.GetBeginAtomId(); in Render()
240 atomIds[1] = bond.GetEndAtomId(); in Render()
259 materials.emplace_back(_elementMaterials[atomicNumbers->GetValue(atomIds[0])]); in Render()
266 materials.emplace_back(_elementMaterials[atomicNumbers->GetValue(atomIds[1])]); in Render()
/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/io/
H A Dcmlformat.cpp186 atomIds[std::string(attribute.value())] = atom.index(); in atoms()
264 begin = atomIds.find(tokens[0]); in bonds()
265 end = atomIds.find(tokens[1]); in bonds()
266 if (begin != atomIds.end() && end != atomIds.end() && in bonds()
403 std::map<std::string, Index> atomIds; member in Avogadro::Io::__anonbe0cb7170211::CmlFormatPrivate
/dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/io/
H A Dcmlformat.cpp186 atomIds[std::string(attribute.value())] = atom.index(); in atoms()
264 begin = atomIds.find(tokens[0]); in bonds()
265 end = atomIds.find(tokens[1]); in bonds()
266 if (begin != atomIds.end() && end != atomIds.end() && in bonds()
403 std::map<std::string, Index> atomIds; member in Avogadro::Io::__anon5d3274410211::CmlFormatPrivate
/dports/science/openbabel/openbabel-3.1.1/src/formats/xml/
H A Dcmlformat.cpp1522 vector<string> atomIds; in WriteMolecule() local
1579 id << " " << atomIds[patom->GetIdx()]; in WriteMolecule()
1827 ref1 = atomIds[pbond->GetBeginAtomIdx()]; in WriteMolecule()
1828 ref2 = atomIds[pbond->GetEndAtomIdx()]; in WriteMolecule()
1858 atomrefs[0] = atomIds[mol.GetAtomById(beginref)->GetIdx()]; in WriteMolecule()
1859 atomrefs[1] = atomIds[mol.GetAtomById(ct_cfg.begin)->GetIdx()]; in WriteMolecule()
1860 atomrefs[2] = atomIds[mol.GetAtomById(ct_cfg.end)->GetIdx()]; in WriteMolecule()
1861 atomrefs[3] = atomIds[mol.GetAtomById(endref)->GetIdx()]; in WriteMolecule()
1900 ref1 += ' ' + atomIds[pbond->GetBeginAtomIdx()]; in WriteMolecule()
1901 ref2 += ' ' + atomIds[pbond->GetEndAtomIdx()]; in WriteMolecule()
[all …]
/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/qtplugins/editor/
H A Deditor.cpp275 Core::Array<Index> atomIds; in reset() local
276 atomIds.push_back(a3); in reset()
277 atomIds.push_back(a2); in reset()
278 atomIds.push_back(a1); in reset()
281 m_molecule->adjustHydrogens(atomIds); in reset()
/dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/qtplugins/editor/
H A Deditor.cpp275 Core::Array<Index> atomIds; in reset() local
276 atomIds.push_back(a3); in reset()
277 atomIds.push_back(a2); in reset()
278 atomIds.push_back(a1); in reset()
281 m_molecule->adjustHydrogens(atomIds); in reset()
/dports/textproc/fox-xml/fox-4.1.2-91-g9c6716e/wcml/test/
H A Dtest_cmlAddMolecule_12.f9024 atomIds=(/"c1", "o1", "h1", "h2"/), bondAtom1Refs=(/"c1", "c1", "c1"/), &
H A Dtest_cmlAddMolecule_13.f9024 atomIds=(/"c1", "o1", "h1", "h2"/), bondAtom1Refs=(/"c1", "c1", "c1", "c1"/), &
H A Dtest_cmlAddMolecule_9.f9024 atomIds=(/"c1", "o1", "h1", "h2"/), bondAtom1Refs=(/"c1", "c1", "c1"/), &

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